From e21086150a30240cc0c0c996e5eb89a3499376b8 Mon Sep 17 00:00:00 2001 From: belegdol Date: Apr 07 2010 21:34:23 +0000 Subject: - Added upstream 1-18 patch --- diff --git a/.cvsignore b/.cvsignore index 80472ff..632621c 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1 +1,2 @@ EMBOSS-6.2.0.tar.gz +patch-1-18.gz diff --git a/EMBOSS.spec b/EMBOSS.spec index fe0cb64..d6263e8 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -18,7 +18,7 @@ Name: EMBOSS Version: 6.2.0 -Release: 2%{?dist} +Release: 3%{?dist} Summary: The European Molecular Biology Open Software Suite Group: Applications/Engineering @@ -33,12 +33,12 @@ Group: Applications/Engineering License: GPLv2+ and LGPLv2+ URL: http://emboss.sf.net/ Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz -#Source1: README.fixes +Source1: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes %if %{with jemboss} Source2: jemboss.desktop %endif # Upstream patch -# Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz +Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-18.gz # Use system-wide pcre. Sent upstream. Patch1: EMBOSS-6.2.0-system-pcre.patch # Use system-wide zlib. @@ -127,7 +127,7 @@ http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/ %prep %setup -q -#%patch0 -p1 +%patch0 -p1 %patch1 -p1 -b .system-pcre %patch2 -p1 -b .system-zlib %patch3 -p1 -b .system-plplot @@ -289,6 +289,9 @@ rm -rf $RPM_BUILD_ROOT %changelog +* Wed Apr 07 2010 Julian Sikorski - 6.2.0-3 +- Added upstream 1-18 patch + * Wed Apr 7 2010 Tom "spot" Callaway - 6.2.0-2 - fix pcre patch, use system pcre - add patch to use system zlib diff --git a/README.fixes b/README.fixes new file mode 100644 index 0000000..dd4d11e --- /dev/null +++ b/README.fixes @@ -0,0 +1,160 @@ +The files in this directory are bugfix replacements for files in +the EMBOSS-6.2.0 distribution. Just drop the replacement files in +the location shown and redo the 'make install.' + +Fix 1. EMBOSS-6.2.0/emboss/jembossctl.c + EMBOSS-6.2.0/jemboss/lib/jemboss.jar + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java + EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java + EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh + +26 Feb 2010: Various Jemboss fixes including allowing multiple + parameters to "wossname" and reporting of stderr + output + + +Fix 2. EMBOSS-6.2.0/emboss/acd/jaspextract.acd + EMBOSS-6.2.0/emboss/acd/jaspscan.acd + EMBOSS-6.2.0/emboss/jaspextract.c + EMBOSS-6.2.0/emboss/jaspscan.c + +26 Feb 2010: jaspextract and jaspscan can use the latest-format data at + http://jaspar.genereg.net/html/DOWNLOAD/Archive.zip + jaspextract uses the data in the "all_data/FlatFileDir" + directory. It is advisable to clear delete any old data files + from your EMBOSS data file area e.g. from the + /usr/local/emboss/share/EMBOSS/data/JASPAR_* directories + + +Fix 3. EMBOSS-6.2.0/emboss/emma.c + +26 Feb 2010: Takes note once again of any EMBOSS_CLUSTALW environment variable + setting. + + +Fix 4. EMBOSS-6.2.0/emboss/acd/trimseq.acd + +26 Feb 2010: Place limit on the maximum window size + + +Fix 5. EMBOSS-6.2.0/ajax/core/ajpat.c + EMBOSS-6.2.0/nucleus/embpat.c + +26 Feb 2010: Fix crash when excessive mismatches requested in one of the + fuzzpro search algorithms. + + +Fix 6. EMBOSS-6.2.0/emboss/coderet.c + EMBOSS-6.2.0/emboss/splitter.c + +26 Feb 2010: Fix crash if no features in the source sequence + + +Fix 7. EMBOSS-6.2.0/emboss/matcher.c + +26 Feb 2010: Fix memory allocation problem + + +Fix 8. EMBOSS-6.2.0/ajax/core/ajseqread.c + EMBOSS-6.2.0/ajax/core/ajseqwrite.c + +01-Mar-2010: Fix sequence format 'refseqp' to be a valid protein + output format and to preserve more fields from refseqp input. + + +Fix 9. EMBOSS-6.2.0/ajax/core/ajlist.c + EMBOSS-6.2.0/ajax/core/ajlist.h + EMBOSS-6.2.0/emboss/showfeat.c + +01-Mar-2010: Fix showfeat sorted feature output to correctly sort exons + for 'join' feature locations. + + +Fix 10.EMBOSS-6.2.0/ajax/graphics/ajgraph.c + EMBOSS-6.2.0/emboss/prettyplot.c + +01-Mar-2010: Fix PNG graphics output format to remove large blank + margins added by the plplot driver. Improve prettyplot + output to better centre sequence characters within boxes. + + +Fix 11.EMBOSS-6.2.0/emboss/recoder.c + EMBOSS-6.2.0/emboss/remap.c + EMBOSS-6.2.0/emboss/restrict.c + EMBOSS-6.2.0/emboss/showseq.c + EMBOSS-6.2.0/emboss/silent.c + +01-Mar-2010: Skip bad enzyme file records + + +Fix 12.EMBOSS-6.2.0/emboss/showpep.c + EMBOSS-6.2.0/emboss/showseq.c + +01-Mar-2010: Correct HTML output closing tag. + + +Fix 13.EMBOSS-6.2.0/ajax/core/ajfeat.c + +01-Mar-2010: Remove warnings for accessions and repeat features in + ensembl format EMBL files. + + +Fix 14.EMBOSS-6.2.0/emboss/acd/cirdna.acd + EMBOSS-6.2.0/emboss/acd/knowntypes.standard + +01-Mar-2010: Fix description of cirdna input + + +Fix 15.EMBOSS-6.2.0/emboss/acd/extractfeat.acd + EMBOSS-6.2.0/emboss/acd/maskfeat.acd + EMBOSS-6.2.0/emboss/acd/showfeat.acd + EMBOSS-6.2.0/emboss/acd/showpep.acd + EMBOSS-6.2.0/emboss/acd/showseq.acd + EMBOSS-6.2.0/emboss/acd/twofeat.acd + EMBOSS-6.2.0/doc/programs/html/extractfeat.html + EMBOSS-6.2.0/doc/programs/html/maskfeat.html + EMBOSS-6.2.0/doc/programs/html/showfeat.html + EMBOSS-6.2.0/doc/programs/html/showpep.html + EMBOSS-6.2.0/doc/programs/html/showseq.html + EMBOSS-6.2.0/doc/programs/html/twofeat.html + EMBOSS-6.2.0/doc/programs/text/extractfeat.txt + EMBOSS-6.2.0/doc/programs/text/maskfeat.txt + EMBOSS-6.2.0/doc/programs/text/showfeat.txt + EMBOSS-6.2.0/doc/programs/text/showpep.txt + EMBOSS-6.2.0/doc/programs/text/showseq.txt + EMBOSS-6.2.0/doc/programs/text/twofeat.txt + +01-Mar-2010: Fix URLs for EMBL/GenBank and SwissProt feature table + descriptions in help and documentation. + + +Fix 16.EMBOSS-6.2.0/emboss/acd/remap.acd + EMBOSS-6.2.0/emboss/acd/restover.acd + EMBOSS-6.2.0/emboss/acd/restrict.acd + EMBOSS-6.2.0/emboss/acd/showseq.acd + +01-Mar-2010: Remove artificial upper limit on number of restriction cuts + + +Fix 17.EMBOSS-6.2.0/doc/programs/html/density.2.density.gif + EMBOSS-6.2.0/doc/programs/html/density.3.density.gif + EMBOSS-6.2.0/doc/programs/html/Makefile.am + EMBOSS-6.2.0/doc/programs/html/Makefile.in + EMBOSS-6.2.0/doc/programs/html/Makefile + +01-Mar-2010: Missing images for density usage examples + + +Fix 18. EMBOSS-6.2.0/ajax/core/ajsys.c + +02-Mar-2010: Add .exe extension when searching for CYGWIN executables diff --git a/sources b/sources index a9e48c6..030cbf8 100644 --- a/sources +++ b/sources @@ -1 +1,2 @@ 2e2937dd0493814ca0f64981f4c79319 EMBOSS-6.2.0.tar.gz +562038e587099462869c45fda2e9628d patch-1-18.gz